Add logging framework (#131)

astrocut/__init__.py

@@ -6,26 +6,33 @@
 from ._astropy_init import *  # noqa
 # ----------------------------------------------------------------------------
 
-# Enforce Python version check during package import.
-# This is the same check as the one at the top of setup.py
-import sys
-
-__minimum_python_version__ = "3.9"
+"""
+This module initializes the astrocut package and performs essential setup tasks, including:
+- Verifying the version of Python.
+- Setting up package-wide logging.
+- Importing key modules.
+"""
 
+import sys
 
-class UnsupportedPythonError(Exception):
-    pass
-
+from .exceptions import UnsupportedPythonError
+from .utils.logger import setup_logger
 
-if sys.version_info < tuple((int(val) for val in __minimum_python_version__.split('.'))):
-    raise UnsupportedPythonError("astrocut does not support Python < {}".format(__minimum_python_version__))
+# Enforce Python version check during package import.
+__minimum_python_version__ = "3.9"  # minimum supported Python version
+if sys.version_info < tuple(map(int, __minimum_python_version__.split('.'))):
+    raise UnsupportedPythonError(f"astrocut does not support Python < {__minimum_python_version__}")
 
+# Initialize package-wide logger using astropy's logging system
+log = setup_logger()
 
+# Import key submodules and functions if not in setup mode
 if not _ASTROPY_SETUP_:  # noqa
     from .make_cube import CubeFactory, TicaCubeFactory  # noqa
     from .cube_cut import CutoutFactory  # noqa
     from .cutouts import fits_cut, img_cut, normalize_img  # noqa
-    from .cutout_processing import (path_to_footprints, center_on_path,  # noqa
-                                    CutoutsCombiner, build_default_combine_function)  # noqa
+    from .cutout_processing import (  # noqa
+        path_to_footprints, center_on_path, CutoutsCombiner, build_default_combine_function  # noqa
+    )  # noqa
     from .asdf_cutouts import asdf_cut, get_center_pixel  # noqa
     from .footprint_cutouts import cube_cut_from_footprint  # noqa

astrocut/asdf_cutouts.py

@@ -16,6 +16,9 @@
 from astropy.coordinates import SkyCoord
 from astropy.modeling import models
 
+from . import log
+from .utils.utils import _handle_verbose
+
 
 def _get_cloud_http(s3_uri: Union[str, S3Path], key: str = None, secret: str = None,
                     token: str = None, verbose: bool = False) -> str:
@@ -41,8 +44,8 @@ def _get_cloud_http(s3_uri: Union[str, S3Path], key: str = None, secret: str = N
     url = f'https://{s3_path.bucket}.s3.amazonaws.com/{s3_path.key}'
     resp = requests.head(url, timeout=10)
     is_anon = False if resp.status_code == 403 else True
-    if verbose and not is_anon:
-        print(f'Attempting to access private S3 bucket: {s3_path.bucket}')
+    if not is_anon:
+        log.debug('Attempting to access private S3 bucket: %s', s3_path.bucket)
 
     # create file system and get URL of file
     fs = s3fs.S3FileSystem(anon=is_anon, key=key, secret=secret, token=token)
@@ -301,6 +304,8 @@ def asdf_cut(input_file: Union[str, pathlib.Path, S3Path], ra: float, dec: float
     astropy.nddata.Cutout2D:
         An image cutout object.
     """
+    # Log messages based on verbosity
+    _handle_verbose(verbose)
 
     # if file comes from AWS cloud bucket, get HTTP URL to open with asdf
     file = input_file

astrocut/cube_cut.py

@@ -6,7 +6,7 @@
 import warnings
 from concurrent.futures import ThreadPoolExecutor
 from itertools import product
-from time import time
+from time import monotonic
 from typing import Any, Dict, Literal, Union
 
 import astropy.units as u
@@ -16,9 +16,10 @@
 from astropy.io import fits
 from astropy.time import Time
 
-from . import __version__
+from . import __version__, log
 from .exceptions import InputWarning, InvalidQueryError
 from .utils.wcs_fitting import fit_wcs_from_points
+from .utils.utils import _handle_verbose
 
 # todo: investigate why for small cutouts the astropy version is not working
 # from astropy.wcs.utils import fit_wcs_from_points
@@ -121,8 +122,7 @@ def _parse_table_info(self, table_data, verbose=False):
                 if data_ind == len(table_data):
                     raise wcs.NoWcsKeywordsFoundError("No FFI rows contain valid WCS keywords.")
 
-        if verbose:
-            print("Using WCS from row {} out of {}".format(data_ind, len(table_data)))
+        log.debug("Using WCS from row %s out of %s", data_ind, len(table_data))
 
         # Turning the table row into a new header object
         wcs_header = fits.header.Header()
@@ -462,10 +462,9 @@ def _get_cutout(self, transposed_cube, threads: Union[int, Literal["auto"]] = 1,
                 uncert_cutout = np.pad(uncert_cutout, padding, 'constant', constant_values=np.nan)
             aperture = np.pad(aperture, padding[1:], 'constant', constant_values=0)
 
-        if verbose:
-            print("Image cutout cube shape: {}".format(img_cutout.shape))
-            if self.product == "SPOC":
-                print("Uncertainty cutout cube shape: {}".format(uncert_cutout.shape))
+        log.debug("Image cutout cube shape: %s", img_cutout.shape)
+        if self.product == "SPOC":
+            log.debug("Uncertainty cutout cube shape: %s", uncert_cutout.shape)
 
         return img_cutout, uncert_cutout, aperture
 
@@ -844,8 +843,9 @@ def cube_cut(
             if unsuccessful returns None.
         """
 
-        if verbose:
-            start_time = time()
+        start_time = monotonic()
+        # Log messages based on verbosity
+        _handle_verbose(verbose)
 
         # Declare the product type being used to make the cutouts
         self.product = product.upper()
@@ -874,9 +874,7 @@ def cube_cut(
             else:
                 self.center_coord = SkyCoord(coordinates, unit='deg')
 
-            if verbose:
-                print("Cutout center coordinate: {},{}".format(self.center_coord.ra.deg,
-                                                               self.center_coord.dec.deg))
+            log.debug("Cutout center coordinate: %s, %s", self.center_coord.ra.deg, self.center_coord.dec.deg)
 
             # Making size into an array [ny, nx]
             if np.isscalar(cutout_size):
@@ -894,10 +892,8 @@ def cube_cut(
 
             # Get cutout limits
             self._get_cutout_limits(cutout_size)
-
-            if verbose:
-                print("xmin,xmax: {}".format(self.cutout_lims[1]))
-                print("ymin,ymax: {}".format(self.cutout_lims[0]))
+            log.debug("xmin,xmax: %s", self.cutout_lims[1])
+            log.debug("ymin,ymax: %s", self.cutout_lims[0])
 
             # Make the cutout
             img_cutout, uncert_cutout, aperture = self._get_cutout(getattr(cube[1], cube_data_prop), threads=threads,
@@ -906,17 +902,15 @@ def cube_cut(
             # Get cutout wcs info
             cutout_wcs_full = self._get_full_cutout_wcs(cube[2].header)
             max_dist, sigma = self._fit_cutout_wcs(cutout_wcs_full, img_cutout.shape[1:])
-            if verbose:
-                print("Maximum distance between approximate and true location: {}".format(max_dist))
-                print("Error in approximate WCS (sigma): {}".format(sigma))
+            log.debug("Maximum distance between approximate and true location: %s", max_dist)
+            log.debug("Error in approximate WCS (sigma): %.4f", sigma)
 
             cutout_wcs_dict = self._get_cutout_wcs_dict()
 
             # Build the TPF
             tpf_object = self._build_tpf(cube, img_cutout, uncert_cutout, cutout_wcs_dict, aperture)
 
-            if verbose:
-                write_time = time()
+            write_time = monotonic()
 
             if not target_pixel_file:
                 _, flename = os.path.split(cube_file)
@@ -931,8 +925,7 @@ def cube_cut(
             target_pixel_file = os.path.join(output_path, target_pixel_file)
 
 
-            if verbose:
-                print("Target pixel file: {}".format(target_pixel_file))
+            log.debug("Target pixel file: %s", target_pixel_file)
 
             # Make sure the output directory exists
             if not os.path.exists(output_path):
@@ -941,8 +934,7 @@ def cube_cut(
             # Write the TPF
             tpf_object.writeto(target_pixel_file, overwrite=True, checksum=True)
 
-        if verbose:
-            print("Write time: {:.2} sec".format(time()-write_time))
-            print("Total time: {:.2} sec".format(time()-start_time))
+        log.debug("Write time: %.2f sec", (monotonic() - write_time))
+        log.debug("Total time: %.2f sec", (monotonic() - start_time))
 
         return target_pixel_file

astrocut/cutout_processing.py

@@ -14,7 +14,8 @@
 
 from scipy.interpolate import splprep, splev
 
-from .utils.utils import get_fits
+from . import log
+from .utils.utils import get_fits, _handle_verbose
 from .exceptions import DataWarning, InvalidInputError
 
 
@@ -148,14 +149,15 @@ def _moving_target_focus(path, size, cutout_fles, verbose=False):
     response : `~astropy.table.Table`
         New cutout table.
     """
+    # Log messages based on verbosity
+    _handle_verbose(verbose)
 
     cutout_table_list = list()
 
     tck_tuple, u = splprep([path["position"].ra, path["position"].dec], u=path["time"].jd, s=0)
 
     for fle in cutout_fles:
-        if verbose:
-            print(fle)
+        log.debug('Processing file: %s', fle)
 
         # Get the stuff we need from the cutout file
         hdu = fits.open(fle)
@@ -373,6 +375,8 @@ def center_on_path(path, size, cutout_fles, target=None, img_wcs=None,
     """
 
     # TODO: add ability to take sizes like in rest of cutout functionality
+    # Log messages based on verbosity
+    _handle_verbose(verbose)
 
     # Performing the path transformation
     cutout_table = _moving_target_focus(path, size, cutout_fles, verbose)